Welcome to #AGA2024!! Here we will share some bits, pieces, and anecdotes from this year’s presidential symposium! Our president Beth Shapiro put together a great list of speakers and we have many excellent poster presenters.
Day 1: AGA Key Distinguished Lecture
This year’s lecture is brought to you by Scott V. Edwards and covers both the newly-sequenced little bush moa genome (which, fun fact, the little bush moa has a full complement of olfactory genes and also does not have protein-related evidence for the loss of flight) and the titular “Pangenomes and conservation genomics: structural variation across a gradient of effective population sizes in North American Scrub-Jays (Aphelocoma)”. What are pangenomes, you may ask? They are essentially genome assemblies of long-read data from individuals within a species that allow scientists to move beyond the use of reference genomes in their work. This allows for discovering genomic differences in areas that may not have sequenced well in the reference or in structural variation between species.
Some fun facts from this talk include:
- The fact that Island Scrub Jays have less genetic diversity than humans (which are notoriously depauperate in the genomic diversity department)
- Jays (as do most Corvids) have A LOT of repetitive sequences in their genome
- Florida, Woodhouse’s, and Island Scrub jays have different genome sizes! Woodhouse’s Scrub Jays have an expanded 18,000 base-pair satellite repeat on their Z chromosome
- Telomeres, which are generally thought to shorten with age, decline in abundance with age in the Florida Scrub Jay
- Island birds have the lowest telomere abundance, which may correlate with small effective population sizes (Brown et al. 2024)
- Looking at depth graphs from pangenomes allows for scanning the genome for chromosomes containing highly repetitive regions (repeats have greater depth than single-copy regions) and for looking for haplotypes with high diversity among individuals
- There appear to be differences in gene copy number variants within scrub jays, where some individuals contain haplotypes that are missing an entire gene
- There may be a correlation between gene copy number and gene expression
- Island birds have the most structural variants out of the scrub jays, which may also be related to their small effective population size and indicative of the genetic load within their small populations
References
Lyda M Brown, Mia C Elbon, Ajay Bharadwaj, Gargi Damle, Joseph Lachance, Does Effective Population Size Govern Evolutionary Differences in Telomere Length?, Genome Biology and Evolution, Volume 16, Issue 5, May 2024, evae111, https://doi.org/10.1093/gbe/evae111